Nucleic Acids Research, Volume 35

Volume 35, Number Database-Issue, January 2007

• Alex Bateman:
  Editorial. 1-2
  

• Michael Y. Galperin:
  The Molecular Biology Database Collection: 2007 update. 3-4
  
• David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Lewis Y. Geer, Yuri Kapustin, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Vadim Miller, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko:
  Database resources of the National Center for Biotechnology Information. 5-12
  
• Hideaki Sugawara, Takashi Abe, Takashi Gojobori, Yoshio Tateno:
  DDBJ working on evaluation and classification of bacterial genes in INSDC. 13-15
  
• Tamara Kulikova, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Lawrence Bower, Paul Browne, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Carola Kanz, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Sheila Plaister, Siamak Sobhany, Peter Stoehr, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler:
  EMBL Nucleotide Sequence Database in 2006. 16-20
  
• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
  GenBank. 21-25
  
• Donna R. Maglott, James Ostell, Kim D. Pruitt, Tatiana A. Tatusova:
  Entrez Gene: gene-centered information at NCBI. 26-31
  
• Christoph Dieterich, M. W. Franz, Martin Vingron:
  Developments in CORG: a gene-centric comparative genomics resource. 32-35
  
• Sunil Archak, Eshwar Meduri, P. Sravana Kumar, Javaregowda Nagaraju:
  InSatDb: a microsatellite database of fully sequenced insect genomes. 36-39
  
• Conrad A. Nieduszynski, Shin-ichiro Hiraga, Prashanth Ak, Craig J. Benham, Anne D. Donaldson:
  OriDB: a DNA replication origin database. 40-46
  
• Byungwook Lee, Taehyung Kim, Seon-Kyu Kim, Kwang Hyung Lee, Doheon Lee:
  Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications. 47-50
  
• Lei Bao, Mi Zhou, Ligang Wu, Lu Lu, Dan Goldowitz, Robert W. Williams, Yan Cui:
  PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. 51-54
  
• John E. Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul M. Harrison, Mark Gerstein:
  Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. 55-60
  
• Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott:
  NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. 61-65
  
• Cristian Chaparro, Romain Guyot, Andrea Zuccolo, Benoît Piégu, Olivier Panaud:
  RetrOryza: a database of the rice LTR-retrotransposons. 66-70
  
• I. Agrafioti, Michael P. H. Stumpf:
  SNPSTR: a database of compound microsatellite-SNP markers. 71-75
  
• Gang Wu, Yuanpu Zheng, Imran Qureshi, Htar Thant Zin, Tyler Beck, Blazej Bulka, Stephen J. Freeland:
  SGDB: a database of synthetic genes re-designed for optimizing protein over-expression. 76-79
  
• Yevgeniy Gelfand, Alfredo Rodriguez, Gary Benson:
  TRDB - The Tandem Repeats Database. 80-87
  
• Axel Visel, Simon Minovitsky, Inna Dubchak, Len A. Pennacchio:
  VISTA Enhancer Browser - a database of tissue-specific human enhancers. 88-92
  
• Namshin Kim, Alexander V. Alekseyenko, Meenakshi Roy, Christopher Lee:
  The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. 93-98
  
• Yeunsook Lee, Younghee Lee, Bumjin Kim, Youngah Shin, Seungyoon Nam, Pora Kim, Namshin Kim, Won-Hyong Chung, Jaesang Kim, Sanghyuk Lee:
  ECgene: an alternative splicing database update. 99-103
  
• Jun-ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Tsuyoshi Kuroda, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi:
  H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. 104-109
  
• Tyler S. Alioto:
  U12DB: a database of orthologous U12-type spliceosomal introns. 110-115
  
• Anil G. Jegga, Jing Chen, Sivakumar Gowrisankar, Mrunal A. Deshmukh, Ranga Chandra Gudivada, Sue Kong, Vivek Kaimal, Bruce J. Aronow:
  GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs. 116-121
  
• Vincent Ferretti, Christian Poitras, Dominique Bergeron, Benoit Coulombe, François Robert, Mathieu Blanchette:
  PReMod: a database of genome-wide mammalian cis-regulatory module predictions. 122-126
  
• Mikhail Pachkov, Ionas Erb, Nacho Molina, Erik van Nimwegen:
  SwissRegulon: a database of genome-wide annotations of regulatory sites. 127-131
  
• Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Julio Collado-Vides:
  Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes. 132-136
  
• C. Jiang, Zhenyu Xuan, Fang Zhao, Michael Q. Zhang:
  TRED: a transcriptional regulatory element database, new entries and other development. 137-140
  
• Tao He, Pufeng Du, Yanda Li:
  dbRES: a web-oriented database for annotated RNA editing sites. 141-144
  
• Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Yuki Kimura, Takashi Komori, Kiyoshi Asai:
  fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. 145-148
  
• Molly Megraw, Praveen Sethupathy, Benoit Corda, Artemis G. Hatzigeorgiou:
  miRGen: a database for the study of animal microRNA genomic organization and function. 149-155
  
• Yong Zhang, Jiongtang Li, Lei Kong, Ge Gao, Qing-Rong Liu, Liping Wei:
  NATsDB: Natural Antisense Transcripts DataBase. 156-161
  
• Maciej Szymanski, Volker A. Erdmann, Jan Barciszewski:
  Noncoding RNAs database (ncRNAdb). 162-164
  
• Ju Youn Lee, Ijen Yeh, Ji Yeon Park, Bin Tian:
  PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. 165-168
  
• James R. Cole, B. Chai, Ryan J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, George M. Garrity, James M. Tiedje:
  The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. 169-172
  
• Ernesto Picardi, Teresa Maria Rosaria Regina, Axel Brennicke, Carla Quagliariello:
  REDIdb: the RNA editing database. 173-177
  
• Ken C. Pang, Stuart Stephen, Marcel E. Dinger, Pär G. Engström, Boris Lenhard, John S. Mattick:
  RNAdb 2.0 - an expanded database of mammalian non-coding RNAs. 178-182
  
• Jun Xie, Ming Zhang, Tao Zhou, Xia Hua, LiSha Tang, Weilin Wu:
  Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs. 183-187
  
• Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, Matthias Platzer:
  TassDB: a database of alternative tandem splice sites. 188-192
  
• The Universal Protein Resource (UniProt). 193-197
  
• Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N. Jorissen, Michael K. Gilson:
  BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. 198-201
  
• Di Wu, Feng Cui, Robert L. Jernigan, Zhijun Wu:
  PIDD: database for Protein Inter-atomic Distance Distributions. 202-207
  
• Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
  eSLDB: eukaryotic subcellular localization database. 208-212
  
• Joshua L. Heazlewood, Robert E. Verboom, Julian Tonti-Filippini, Ian Small, A. Harvey Millar:
  SUBA: the Arabidopsis Subcellular Database. 213-218
  
• Gonzalo López, Alfonso Valencia, Michael L. Tress:
  FireDB - a database of functionally important residues from proteins of known structure. 219-223
  
• Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Virginie Buillard, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Louise Daugherty, Mark Dibley, Robert D. Finn, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicolas Hulo, Sarah Hunter, Daniel Kahn, Alexander Kanapin, Anish Kejariwal, Alberto Labarga, Petra S. Langendijk-Genevaux, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Christine A. Orengo, Robert Petryszak, Jeremy D. Selengut, Christian J. A. Sigrist, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats:
  New developments in the InterPro database. 224-228
  
• Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, Manuela Helmer-Citterich:
  Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. 229-231
  
• Paolo Sonego, Mircea Pacurar, Somdutta Dhir, Attila Kertész-Farkas, András Kocsor, Zoltán Gáspári, Jack A. M. Leunissen, Sándor Pongor:
  A Protein Classification Benchmark collection for machine learning. 232-236
  
• Aron Marchler-Bauer, John B. Anderson, Myra K. Derbyshire, Carol DeWeese-Scott, Noreen R. Gonzales, Marc Gwadz, Luning Hao, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Dmitri M. Krylov, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Shennan Lu, Gabriele H. Marchler, Mikhail Mullokandov, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, Stephen H. Bryant:
  CDD: a conserved domain database for interactive domain family analysis. 237-240
  
• Elon Portugaly, Nathan Linial, Michal Linial:
  EVEREST: a collection of evolutionary conserved protein domains. 241-246
  
• Huaiyu Mi, Nan Guo, Anish Kejariwal, Paul D. Thomas:
  PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. 247-252
  
• Antonina Andreeva, Andreas Prlic, Tim J. P. Hubbard, Alexey G. Murzin:
  SISYPHUS - structural alignments for proteins with non-trivial relationships. 253-259
  
• Jeremy D. Selengut, Daniel H. Haft, Tanja Davidsen, Anurhada Ganapathy, Michelle Gwinn-Giglio, William C. Nelson, Alexander R. Richter, Owen White:
  TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. 260-264
  
• Shalin Seebah, Anita Suresh, Shaowei Zhuo, Yong How Choong, Hazel Chua, Danny Chuon, Roger Beuerman, Chandra Verma:
  Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides. 265-268
  
• Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
  REBASE - enzymes and genes for DNA restriction and modification. 269-270
  
• Mark D'Souza, Elizabeth M. Glass, Mustafa H. Syed, Yi Zhang, Alexis A. Rodriguez, Natalia Maltsev, Michael Y. Galperin:
  Sentra: a database of signal transduction proteins for comparative genome analysis. 271-273
  
• Qinghu Ren, Kaixi Chen, Ian T. Paulsen:
  TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. 274-279
  
• Philip Toukach, Hiren J. Joshi, René Ranzinger, Yuri Knirel, Claus-Wilhelm von der Lieth:
  Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de. 280-286
  
• M. Frank, T. Lütteke, C.-W. von der Lieth:
  GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages. 287-290
  
• Lesley H. Greene, Tony E. Lewis, Sarah Addou, Alison L. Cuff, Timothy Dallman, Mark Dibley, Oliver Redfern, Frances M. G. Pearl, Rekha Nambudiry, Adam Reid, Ian Sillitoe, Corin Yeats, Janet M. Thornton, Christine A. Orengo:
  The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. 291-297
  
• Yanli Wang, Kenneth J. Addess, Jie Chen, Lewis Y. Geer, Jane He, Siqian He, Shennan Lu, Thomas Madej, Aron Marchler-Bauer, Paul A. Thiessen, Naigong Zhang, Stephen H. Bryant:
  MMDB: annotating protein sequences with Entrez's 3D-structure database. 298-300
  
• Helen M. Berman, Kim Henrick, Haruki Nakamura, John L. Markley:
  The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. 301-303
  
• Kate F. Fulton, Mark A. Bate, Noel G. Faux, Khalid Mahmood, Chris Betts, Ashley M. Buckle:
  Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium. 304-307
  
• Derek Wilson, Martin Madera, Christine Vogel, Cyrus Chothia, Julian Gough:
  The SUPERFAMILY database in 2007: families and functions. 308-313
  
• M. Michael Gromiha, Yukimitsu Yabuki, Srinesh Kundu, Sivasundaram Suharnan, Makiko Suwa:
  TMBETA-GENOME: database for annotated ß-barrel membrane proteins in genomic sequences. 314-316
  
• Chesley M. Leslin, Alexej Abyzov, Valentin A. Ilyin:
  TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. 317-321
  
• Gil Alterovitz, Michael Xiang, Mamta Mohan, Marco Ramoni:
  GO PaD: the Gene Ontology Partition Database. 322-327
  
• Yuying Tian, Allan W. Dickerman:
  GeneTrees: a phylogenomics resource for prokaryotes. 328-331
  
• T. Ryan Gregory, James A. Nicol, Heidi Tamm, Bellis Kullman, Kaur Kullman, Ilia J. Leitch, Brian G. Murray, Donald F. Kapraun, Johann Greilhuber, Michael D. Bennett:
  Eukaryotic genome size databases. 332-338
  
• Masaki Hirahata, Takashi Abe, Naoto Tanaka, Yoshikazu Kuwana, Yasumasa Shigemoto, Satoru Miyazaki, Yoshiyuki Suzuki, Hideaki Sugawara:
  Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes. 339-342
  
• Ikuo Uchiyama:
  MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. 343-346
  
• Leslie Klis McNeil, Claudia Reich, Ramy K. Aziz, Daniela Bartels, Matthew Cohoon, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Kaitlyn Hwang, Michael Kubal, Gohar Rem Margaryan, Folker Meyer, William Mihalo, Gary J. Olsen, Robert Olson, Andrei Osterman, Daniel Paarmann, Tobias Paczian, Bruce D. Parrello, Gordon D. Pusch, Dmitry A. Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross A. Overbeek, Rick Stevens:
  The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. 347-353
  
• M. Louise Riley, Thorsten Schmidt, Irena I. Artamonova, Christian Wagner, Andreas Volz, Klaus Heumann, Hans-Werner Mewes, Dmitrij Frishman:
  PEDANT genome database: 10 years online. 354-357
  
• Christian von Mering, Lars Juhl Jensen, Michael Kuhn, Samuel Chaffron, Tobias Doerks, Beate Krüger, Berend Snel, Peer Bork:
  STRING 7 - recent developments in the integration and prediction of protein interactions. 358-362
  
• Christophe Combet, Nicolas Garnier, Céline Charavay, Delphine Grando, Daniel Crisan, Julien Lopez, Alexandre Dehne-Garcia, Christophe Geourjon, Emmanuel Bettler, Chantal Hulo, Philippe Le Mercier, Ralf Bartenschlager, Helmut Diepolder, Darius Moradpour, Jean-Michel Pawlotsky, Charles M. Rice, Christian Trépo, François Penin, Gilbert Deléage:
  euHCVdb: the European hepatitis C virus database. 363-366
  
• Saravanamuttu Gnaneshan, Samreen Ijaz, Joanne Moran, Mary Ramsay, Jonathan Green:
  HepSEQ: International Public Health Repository for Hepatitis B. 367-370
  
• Calvin Pan, Joseph Kim, Lamei Chen, Qi Wang, Christopher Lee:
  The HIV positive selection mutation database. 371-375
  
• Suhua Chang, Jiajie Zhang, Xiaoyun Liao, Xinxing Zhu, Dahai Wang, Jiang Zhu, Tao Feng, Baoli Zhu, George F. Gao, Jian Wang, Huanming Yang, Jun Yu, Jing Wang:
  Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. 376-380
  
• Paul Wei-Che Hsu, Li-Zen Lin, Sheng-Da Hsu, Justin Bo-Kai Hsu, Hsien-Da Huang:
  ViTa: prediction of host microRNAs targets on viruses. 381-385
  
• Luke E. Ulrich, Igor B. Zhulin:
  MiST: a microbial signal transduction database. 386-390
  
• Carol L. Ecale Zhou, Jason Smith, Marisa Lam, Adam Zemla, Matthew D. Dyer, Tom Slezak:
  MvirDB - a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. 391-394
  
• Sung Ho Yoon, Young-Kyu Park, Soohyun Lee, Doil Choi, Tae Kwang Oh, Cheol-Goo Hur, Jihyun F. Kim:
  Towards pathogenomics: a web-based resource for pathogenicity islands. 395-400
  
• E. E. Snyder, N. Kampanya, J. Lu, Eric K. Nordberg, H. R. Karur, Maulik Shukla, Jeetendra Soneja, Y. Tian, Tian Xue, H. Yoo, F. Zhang, C. Dharmanolla, N. V. Dongre, J. J. Gillespie, J. Hamelius, M. Hance, K. I. Huntington, D. Jukneliene, J. Koziski, L. Mackasmiel, S. P. Mane, V. Nguyen, A. Purkayastha, J. Shallom, G. Yu, Y. Guo, Joseph L. Gabbard, D. Hix, A. F. Azad, S. C. Baker, S. M. Boyle, Y. Khudyakov, X. J. Meng, C. Rupprecht, J. Vinje, Oswald Crasta, M. J. Czar, Allan Dickerman, J. Dana Eckart, Ron Kenyon, Rebecca Will, J. C. Setubal, Bruno W. S. Sobral:
  PATRIC: The VBI PathoSystems Resource Integration Center. 401-406
  
• Alexei E. Kazakov, Michael J. Cipriano, Pavel S. Novichkov, Simon Minovitsky, Dmitry V. Vinogradov, Adam P. Arkin, Andrey A. Mironov, Mikhail S. Gelfand, Inna Dubchak:
  RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. 407-412
  
• Kim Brügger:
  The Sulfolobus database. 413-415
  
• Chia-Hung Chang, Yu-Chung Chang, Anthony Underwood, Chien-Shun Chiou, Cheng-Yan Kao:
  VNTRDB: a bacterial variable number tandem repeat locus database. 416-421
  
• Bradley I. Arshinoff, Garret Suen, Eric M. Just, Sohel M. Merchant, Warren A. Kibbe, Rex L. Chisholm, Roy D. Welch:
  Xanthusbase: adapting wikipedia principles to a model organism database. 422-426
  
• Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer, Philippa Rhodes, John A. Miller, Eileen Kraemer, Christian J. Stoeckert Jr., David S. Roos, Jessica C. Kissinger:
  ApiDB: integrated resources for the apicomplexan bioinformatics resource center. 427-430
  
• Junichi Watanabe, Hiroyuki Wakaguri, Masahide Sasaki, Yutaka Suzuki, Sumio Sugano:
  Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs. 431-438
  
• Olivier Arnaiz, Scott Cain, Jean Cohen, Linda Sperling:
  ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. 439-444
  
• Emmet A. O'Brien, Liisa B. Koski, Yue Zhang, LiuSong Yang, Eric Wang, Michael W. Gray, Gertraud Burger, B. Franz Lang:
  TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). 445-451
  
• Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Prachi Shah, Gail Binkley, Christopher Lane, Stuart R. Miyasato, Gavin Sherlock:
  Sequence resources at the Candida Genome Database. 452-456
  
• Alexandre Gattiker, Christa Niederhauser-Wiederkehr, James Moore, Leandro Hermida, Michael Primig:
  The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction. 457-462
  
• Luciano Fernandez-Ricaud, Jonas Warringer, Elke Ericson, Kerstin Glaab, Pär Davidsson, Fabian Nilsson, Graham J. L. Kemp, Olle Nerman, Anders Blomberg:
  PROPHECY - a yeast phenome database, update 2006. 463-467
  
• Robert S. Nash, Shuai Weng, Benjamin C. Hitz, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Michael S. Livstone, Rose Oughtred, Julie Park, Marek S. Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Stuart R. Miyasato, Anand Sethuraman, Mark Schroeder, Kara Dolinski, David Botstein, J. Michael Cherry:
  Expanded protein information at SGD: new pages and proteome browser. 468-471
  
• Lisa R. Girard, Tristan J. Fiedler, Todd W. Harris, Felicia Carvalho, Igor Antoshechkin, Michael Han, Paul W. Sternberg, Lincoln D. Stein, Martin Chalfie:
  WormBook: the online review of Caenorhabditis elegans biology. 472-475
  
• Liangjiang Wang, Suzhi Wang, Yonghua Li, Martin S. R. Paradesi, Susan J. Brown:
  BeetleBase: the model organism database for Tribolium castaneum. 476-479
  
• Donald G. Gilbert:
  DroSpeGe: rapid access database for new Drosophila species genomes. 480-485
  
• Madeline A. Crosby, Joshua L. Goodman, Victor B. Strelets, Peili Zhang, William M. Gelbart:
  FlyBase: genomes by the dozen. 486-491
  
• Thomas Horn, Zeynep Arziman, Juerg Berger, Michael Boutros:
  GenomeRNAi: a database for cell-based RNAi phenotypes. 492-497
  
• Christoph Dieterich, Waltraud Roeseler, Patrick Sobetzko, Ralf J. Sommer:
  Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus. 498-502
  
• Daniel Lawson, Peter Arensburger, Peter Atkinson, Nora J. Besansky, Robert V. Bruggner, Ryan Butler, Kathryn S. Campbell, George K. Christophides, Scott Christley, Emmanuel Dialynas, David Emmert, Martin Hammond, Catherine A. Hill, Ryan C. Kennedy, Neil F. Lobo, Robert M. MacCallum, Gregory R. Madey, Karine Megy, Seth Redmond, Susan Russo, David W. Severson, Eric O. Stinson, Pantelis Topalis, Evgeni M. Zdobnov, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, Frank H. Collins:
  VectorBase: a home for invertebrate vectors of human pathogens. 503-505
  
• Tamberlyn Bieri, Darin Blasiar, Philip Ozersky, Igor Antoshechkin, Carol Bastiani, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis, Tristan J. Fiedler, Lisa R. Girard, Michael Han, Todd W. Harris, Ranjana Kishore, Raymond Lee, Sheldon J. McKay, Hans-Michael Müller, Cecilia Nakamura, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. Schwarz, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Richard Durbin, Lincoln D. Stein, Paul W. Sternberg, John Spieth:
  WormBase: new content and better access. 506-510
  
• Jens Barthelmes, Christian Ebeling, Antje Chang, Ida Schomburg, Dietmar Schomburg:
  BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. 511-514
  
• Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, Noel M. O'Boyle, James W. Torrance, Peter Murray-Rust, John B. O. Mitchell, Janet M. Thornton:
  MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. 515-520
  
• David S. Wishart, Dan Tzur, Craig Knox, Roman Eisner, Anchi Guo, Nelson Young, Dean Cheng, Kevin Jewell, David Arndt, Summit Sawhney, Chris Fung, Lisa Nikolai, Mike Lewis, Marie-Aude Coutouly, Ian J. Forsythe, Peter Tang, Savita Shrivastava, Kevin Jeroncic, Paul Stothard, Godwin Amegbey, David Block, David D. Hau, James Wagner, Jessica Miniaci, Melisa Clements, Mulu Gebremedhin, Natalie Guo, Ying Zhang, Gavin E. Duggan, Glen D. MacInnis, Alim M. Weljie, Reza Dowlatabadi, Fiona Bamforth, Derrick Clive, Russell Greiner, Liang Li, Tom Marrie, Brian D. Sykes, Hans J. Vogel, Lori Querengesser:
  HMDB: the Human Metabolome Database. 521-526
  
• Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward A. Dennis, Christopher K. Glass, Alfred H. Merrill Jr., Robert C. Murphy, Christian R. H. Raetz, David W. Russell, Shankar Subramaniam:
  LMSD: LIPID MAPS structure database. 527-532
  
• Claudia Choi, Richard Münch, Stefan Leupold, Johannes Klein, Inga Siegel, Bernhard Thielen, Beatrice Benkert, Martin Kucklick, Max Schobert, Jens Barthelmes, Christian Ebeling, Isam Haddad, Maurice Scheer, Andreas Grote, Karsten Hiller, Boyke Bunk, Kerstin Schreiber, Ida Retter, Dietmar Schomburg, Dieter Jahn:
  SYSTOMONAS - an integrated database for systems biology analysis of Pseudomonas. 533-537
  
• H. Craig Mak, Mike Daly, Bianca Gruebel, Trey Ideker:
  CellCircuits: a database of protein network models. 538-545
  
• Yoshinobu Igarashi, Alexey M. Eroshkin, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Jeffrey W. Smith, Andrei Osterman, Adam Godzik:
  CutDB: a proteolytic event database. 546-549
  
• Fedor Kolpakov, Vladimir Poroikov, Ruslan N. Sharipov, Yury V. Kondrakhin, Alexey Zakharov, Alexey Lagunin, Luciano Milanesi, Alexander E. Kel:
  CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. 550-556
  
• Arnaud Ceol, Andrew Chatr-aryamontri, Elena Santonico, Roberto Sacco, Luisa Castagnoli, Gianni Cesareni:
  DOMINO: a database of domain-peptide interactions. 557-560
  
• Samuel Kerrien, Y. Alam-Faruque, B. Aranda, I. Bancarz, A. Bridge, C. Derow, Emily Dimmer, M. Feuermann, A. Friedrichsen, Rachael P. Huntley, C. Kohler, J. Khadake, C. Leroy, A. Liban, C. Lieftink, Luisa Montecchi-Palazzi, Sandra E. Orchard, J. Risse, K. Robbe, Bernd Roechert, David Thorneycroft, Y. Zhang, Rolf Apweiler, Henning Hermjakob:
  IntAct - open source resource for molecular interaction data. 561-565
  
• Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian D. Athey, David J. States, H. V. Jagadish:
  Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. 566-571
  
• Andrew Chatr-aryamontri, Arnaud Ceol, Luisa Montecchi-Palazzi, Giuliano Nardelli, Maria Victoria Schneider, Luisa Castagnoli, Gianni Cesareni:
  MINT: the Molecular INTeraction database. 572-574
  
• Petras J. Kundrotas, Emil Alexov:
  PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. 575-579
  
• Emily R. Jefferson, Thomas P. Walsh, Timothy J. Roberts, Geoffrey J. Barton:
  SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. 580-589
  
• Gautam Chaurasia, Yasir Iqbal, Christian Hänig, Hanspeter Herzel, Erich E. Wanker, Matthias E. Futschik:
  UniHI: an entry gate to the human protein interactome. 590-594
  
• Kieran Hervold, Andrew Martin, Roger A. Kirkpatrick, Paul F. Mc Kenna, F. A. Ramirez-Weber:
  Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community. 595-598
  
• Fiona M. McCarthy, Susan M. Bridges, Nan Wang, G. Bryce Magee, W. Paul Williams, Dawn S. Luthe, Shane C. Burgess:
  AgBase: a unified resource for functional analysis in agriculture. 599-603
  
• Zhi-Liang Hu, Eric Ryan Fritz, James M. Reecy:
  AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. 604-609
  
• Tim J. P. Hubbard, Bronwen L. Aken, Kathryn Beal, Benoit Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Fiona Cunningham, Tim Cutts, Thomas Down, S. C. Dyer, Stephen Fitzgerald, Julio Fernandez-Banet, Stefan Gräf, Syed Haider, Martin Hammond, Javier Herrero, Richard C. G. Holland, Kevin L. Howe, Kerstin Howe, Nathan Johnson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Craig Melsopp, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Andreas Prlic, S. Rice, Daniel Rios, Michael Schuster, I. Sealy, Jessica Severin, Guy Slater, Damian Smedley, Giulietta Spudich, S. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, M. Wood, Tony Cox, Val Curwen, Richard Durbin, Xosé M. Fernández-Suarez, Paul Flicek, Arek Kasprzyk, Glenn Proctor, Stephen M. J. Searle, James Smith, Abel Ureta-Vidal, Ewan Birney:
  Ensembl 2007. 610-617
  
• Constance M. Smith, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald:
  The mouse Gene Expression Database (GXD): 2007 update. 618-623
  
• Raquel Egea, Sònia Casillas, Enol Fernández, Miquel Àngel Senar, Antonio Barbadilla:
  MamPol: a database of nucleotide polymorphism in the Mammalia class. 624-629
  
• Janan T. Eppig, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson:
  The mouse genome database (MGD): new features facilitating a model system. 630-637
  
• Dale A. Begley, Debra M. Krupke, Matthew J. Vincent, John P. Sundberg, Carol J. Bult, Janan T. Eppig:
  Mouse Tumor Biology Database (MTB): status update and future directions. 638-642
  
• Molly A. Bogue, Stephen C. Grubb, Terry P. Maddatu, Carol J. Bult:
  Mouse Phenome Database (MPD). 643-649
  
• Hirohide Uenishi, Tomoko Eguchi-Ogawa, Hiroki Shinkai, Naohiko Okumura, Kohei Suzuki, Daisuke Toki, Noriyuki Hamasima, Takashi Awata:
  PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences. 650-653
  
• Jue Ruan, Yiran Guo, Heng Li, Yafeng Hu, Fei Song, Xin Huang, Karsten Kristiansen, Lars Bolund, Jun Wang:
  PigGIS: Pig Genomic Informatics System. 654-657
  
• Simon N. Twigger, Mary Shimoyama, Susan Bromberg, Anne E. Kwitek, Howard J. Jacob:
  The Rat Genome Database, update 2007 - Easing the path from disease to data and back again. 658-662
  
• Daryl J. Thomas, Kate R. Rosenbloom, Hiram Clawson, Angie S. Hinrichs, Heather Trumbower, Brian J. Raney, Donna Karolchik, Galt P. Barber, Rachel A. Harte, Jennifer Hillman-Jackson, Robert M. Kuhn, Brooke L. Rhead, Kayla E. Smith, Archana Thakkapallayil, Ann S. Zweig, David Haussler, W. James Kent:
  The ENCODE Project at UC Santa Cruz. 663-667
  
• Robert M. Kuhn, Donna Karolchik, Ann S. Zweig, Heather Trumbower, Daryl J. Thomas, Archana Thakkapallayil, Charles W. Sugnet, Mario Stanke, Kayla E. Smith, Adam C. Siepel, Kate R. Rosenbloom, Brooke L. Rhead, Brian J. Raney, Andy Pohl, J. S. Pedersen, Fan Hsu, Angela S. Hinrichs, Rachel A. Harte, Mark Diekhans, Hiram Clawson, Gill Bejerano, Galt P. Barber, Robert Baertsch, David Haussler, W. James Kent:
  The UCSC genome browser database: update 2007. 668-673
  
• Alecksandr Kutchma, Nayeem Quayum, Jan Jensen:
  GeneSpeed: protein domain organization of the transcriptome. 674-679
  
• Dongmei Zuo, Stephanie E. Mohr, Yanhui Hu, Elena Taycher, Andreas Rolfs, Jason Kramer, Janice Williamson, Joshua LaBaer:
  PlasmID: a centralized repository for plasmid clone information and distribution. 680-684
  
• Koichiro Higasa, Katsuyuki Miyatake, Yoji Kukita, Tomoko Tahira, Kenshi Hayashi:
  D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples. 685-689
  
• Sjozef van Baal, Polynikis Kaimakis, Manyphong Phommarinh, Daphne Koumbi, Harry Cuppens, Francesca Riccardino, Milan Macek Jr., Charles R. Scriver, George P. Patrinos:
  FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide. 690-695
  
• Philip Groth, Nadia Pavlova, Ivan Kalev, Spas Tonov, Georgi Georgiev, Hans-Dieter Pohlenz, Bertram Weiss:
  PhenomicDB: a new cross-species genotype/phenotype resource. 696-699
  
• Anil G. Jegga, Sivakumar Gowrisankar, Jing Chen, Bruce J. Aronow:
  PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. 700-706
  
• Shengting Li, Lijia Ma, Heng Li, Søren Vang, Yafeng Hu, Lars Bolund, Jun Wang:
  Snap: an integrated SNP annotation platform. 707-710
  
• Jungsun Park, Sohyun Hwang, Yong Seok Lee, Sang-Cheol Kim, Doheon Lee:
  SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms. 711-715
  
• Daryl J. Thomas, Heather Trumbower, Andrew D. Kern, Brooke L. Rhead, Robert M. Kuhn, David Haussler, W. James Kent:
  Variation resources at UC Santa Cruz. 716-720
  
• Maureen E. Higgins, Martine Claremont, John E. Major, Chris Sander, Alex E. Lash:
  CancerGenes: a gene selection resource for cancer genome projects. 721-726
  
• Wen-Hui Su, Chuan-Chuan Chao, Shiou-Hwei Yeh, Ding-Shinn Chen, Pei-Jer Chen, Yuh-Shan Jou:
  OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci. 727-731
  
• Suisheng Tang, Zhuo Zhang, Sin Lam Tan, Man-Hung Eric Tang, Arun Prashanth Kumar, Suresh Kumar Ramadoss, Vladimir B. Bajic:
  KBERG: KnowledgeBase for Estrogen Responsive Genes. 732-736
  
• Wuxue Zhang, Yong Zhang, Hui Zheng, Chen Zhang, Wei Xiong, John G. Olyarchuk, Michael G. Walker, Weifeng Xu, Min Zhao, Shuqi Zhao, Zhuan Zhou, Liping Wei:
  SynDB: a Synapse protein DataBase based on synapse ontology. 737-741
  
• Erin M. Hulbert, Luc J. Smink, Ellen C. Adlem, James E. Allen, David B. Burdick, Oliver S. Burren, Christopher C. Cavnor, Geoffrey E. Dolman, Daisy Flamez, Karen F. Friery, Barry C. Healy, Sarah A. Killcoyne, Burak Kutlu, Helen Schuilenburg, Neil M. Walker, Josyf Mychaleckyj, Decio L. Eizirik, Linda S. Wicker, John A. Todd, Nathan Goodman:
  T1DBase: integration and presentation of complex data for type 1 diabetes research. 742-746
  
• Helen E. Parkinson, Misha Kapushesky, Mohammadreza Shojatalab, Niran Abeygunawardena, Richard Coulson, Anna Farne, Ele Holloway, N. Kolesnykov, P. Lilja, Margus Lukk, Roby Mani, Tim F. Rayner, Anjan Sharma, E. William, Ugis Sarkans, Alvis Brazma:
  ArrayExpress - a public database of microarray experiments and gene expression profiles. 747-750
  
• Joan M. Mazzarelli, John Brestelli, Regina K. Gorski, Junmin Liu, Elisabetta Manduchi, Deborah F. Pinney, Jonathan Schug, Peter White, Klaus H. Kaestner, Christian J. Stoeckert Jr.:
  EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. 751-755
  
• Fei Pan, Chi-Hsien Chiu, Sudip Pulapura, Michael R. Mehan, Juan Nunez-Iglesias, Kangyu Zhang, Kiran Kamath, Michael S. Waterman, Caleb E. Finch, Xianghong Jasmine Zhou:
  Gene Aging Nexus: a web database and data mining platform for microarray data on aging. 756-759
  
• Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F. Kim, Alexandra Soboleva, Maxim Tomashevsky, Ron Edgar:
  NCBI GEO: mining tens of millions of expression profiles - database and tools update. 760-765
  
• Janos Demeter, Catherine Beauheim, Jeremy Gollub, Tina Hernandez-Boussard, Heng Jin, Donald Maier, John C. Matese, Michael Nitzberg, Farrell Wymore, Zachariah K. Zachariah, Patrick O. Brown, Gavin Sherlock, Catherine A. Ball:
  The Stanford Microarray Database: implementation of new analysis tools and open source release of software. 766-770
  
• Yanling Zhang, Yong Zhang, Jun Adachi, Jesper V. Olsen, Rong Shi, Gustavo de Souza, Erica Pasini, Leonard J. Foster, Boris Macek, Alexandre Zougman, Chanchal Kumar, Jacek R. Wisniewski, Jan Wang, Matthias Mann:
  MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes. 771-779
  
• Yi-Bu Chen, Ansuman Chattopadhyay, Phillip Bergen, Cynthia Gadd, Nancy Tannery:
  The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System - a one-stop gateway to online bioinformatics databases and software tools. 780-785
  
• Megan Sickmeier, Justin A. Hamilton, Tanguy LeGall, Vladimir Vacic, Marc S. Cortese, Agnes Tantos, Beata Szabo, Peter Tompa, Jake Yue Chen, Vladimir N. Uversky, Zoran Obradovic, A. Keith Dunker:
  DisProt: the Database of Disordered Proteins. 786-793
  
• C. J. Zheng, L. Y. Han, B. Xie, C. Y. Liew, S. Ong, J. Cui, H. L. Zhang, Z. Q. Tang, S. H. Gan, L. Jiang, Yu Zong Chen:
  PharmGED: Pharmacogenetic Effect Database. 794-799
  
• Alexander Loy, Frank Maixner, Michael Wagner, Matthias Horn:
  probeBase - an online resource for rRNA-targeted oligonucleotide probes: new features 2007. 800-804
  
• Wenwu Cui, Dennis D. Taub, Kevin Gardner:
  qPrimerDepot: a primer database for quantitative real time PCR. 805-809
  
• Nuwee Wiwatwattana, Christopher M. Landau, G. Jamie Cope, Gabriel A. Harp, Anuj Kumar:
  Organelle DB: an updated resource of eukaryotic protein localization and function. 810-814
  
• Agatha Schlüter, Stéphane Fourcade, Enric Domènech-Estévez, Toni Gabaldón, Jaime Huerta-Cepas, Guillaume Berthommier, Raymond Ripp, Ronald J. A. Wanders, Olivier Poch, Aurora Pujol:
  PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease. 815-822
  
• Eduardo Ruiz-Pesini, Marie T. Lott, Vincent Procaccio, Jason C. Poole, Marty C. Brandon, Dan Mishmar, Christina Yi, James Kreuziger, Pierre Baldi, Douglas C. Wallace:
  An enhanced MITOMAP with a global mtDNA mutational phylogeny. 823-828
  
• Cameron Johnson, Lewis Bowman, Alex T. Adai, Vicki Vance, Venkatesan Sundaresan:
  CSRDB: a small RNA integrated database and browser resource for cereals. 829-833
  
• Manuel Spannagl, Octave Noubibou, Dirk Haase, Li Yang, Heidrun Gundlach, Tobias Hindemitt, Kathrin Klee, Georg Haberer, Heiko Schoof, Klaus F. X. Mayer:
  MIPSPlantsDB - plant database resource for integrative and comparative plant genome research. 834-840
  
• Lorenz Bülow, Martin Schindler, Reinhard Hehl:
  PathoPlant^®: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses. 841-845
  
• Kevin L. Childs, John P. Hamilton, Wei Zhu, Eugene Ly, Foo Cheung, Hank Wu, Pablo D. Rabinowicz, Chris D. Town, C. Robin Buell, Agnes P. Chan:
  The TIGR Plant Transcript Assemblies database. 846-851
  
• Nigel S. Walker, Nicholas Stiffler, Alice Barkan:
  POGs/PlantRBP: a resource for comparative genomics in plants. 852-856
  
• Claudia Galuschka, Martin Schindler, Lorenz Bülow, Reinhard Hehl:
  AthaMap web tools for the analysis and identification of co-regulated genes. 857-862
  
• Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi, Motoshi Saeki, Daisuke Shibata, Kazuki Saito, Hiroyuki Ohta:
  ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. 863-869
  
• Timothy A. Erwin, Erica G. Jewell, Christopher G. Love, Geraldine A. C. Lim, Xi Li, Ross Chapman, Jacqueline Batley, Jason E. Stajich, Emmanuel Mongin, Elia Stupka, Bruce Ross, German C. Spangenberg, David Edwards:
  BASC: an integrated bioinformatics system for Brassica research. 870-873
  
• Yong Li, Mario G. Rosso, Prisca Viehoever, Bernd Weisshaar:
  GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions. 874-878
  
• Huazong Zeng, Lijun Luo, Weixiong Zhang, Jie Zhou, Zuofeng Li, Hongyan Liu, Tiansheng Zhu, Xiangqian Feng, Yang Zhong:
  PlantQTL-GE: a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information. 879-882
  
• Shu Ouyang, Wei Zhu, John A. Hamilton Jr., Haining Lin, Matthew Campbell, Kevin L. Childs, Françoise Thibaud-Nissen, Renae L. Malek, Yuandan Lee, Li Zheng, Joshua Orvis, Brian Haas, Jennifer R. Wortman, C. Robin Buell:
  The TIGR Rice Genome Annotation Resource: improvements and new features. 883-887
  
• Nathalie Pavy, James J. Johnson, John A. Crow, Charles Paule, Timothy M. Kunau, John MacKay, Ernest F. Retzel:
  ForestTreeDB: a database dedicated to the mining of tree transcriptomes. 888-894
  
• Carolyn J. Lawrence, Mary L. Schaeffer, Trent E. Seigfried, Darwin A. Campbell, Lisa C. Harper:
  MaizeGDB's new data types, resources and activities. 895-900
  
• Nunzio D'Agostino, Mario Aversano, Luigi Frusciante, Maria Luisa Chiusano:
  TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species. 901-905
  
• Stefan Günther, Dorothea Hempel, Mathias Dunkel, Kristian Rother, Robert Preissner:
  SuperHapten: a comprehensive database for small immunogenic compounds. 906-910
  

Volume 35, Number Web-Server-Issue, July 2007

• Gary Benson:
  Editorial. 1
  

• Joanne A. Fox, Scott McMillan, B. F. Francis Ouellette:
  Conducting Research on the Web: 2007 Update for the Bioinformatics Links Directory. 3-5
  
• Alberto Labarga, Franck Valentin, Mikael Andersson, Rodrigo Lopez:
  Web Services at the European Bioinformatics Institute. 6-11
  
• Mounir Errami, Jonathan D. Wren, Justin M. Hicks, Harold R. Garner:
  eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications. 12-15
  
• Ildefonso Cases, David G. Pisano, Eduardo Andrés León, Angel Carro, José María Fernández, Gonzalo Gómez-López, Jose M. Rodriguez, Jaime F. Vera, Alfonso Valencia, Ana María Rojas:
  CARGO: a web portal to integrate customized biological information. 16-20
  
• José M. Fernández, Robert Hoffmann, Alfonso Valencia:
  iHOP web services. 21-26
  
• Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy, Kimmen Sjölander:
  Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis. 27-32
  
• Thomas M. Keane, Thomas J. Naughton, James O. McInerney:
  MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. 33-37
  
• Joaquín Tárraga, Ignacio Medina, Leonardo Arbiza, Jaime Huerta-Cepas, Toni Gabaldón, Joaquín Dopazo, Hernán Dopazo:
  Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. 38-42
  
• Warren A. Kibbe:
  OligoCalc: an online oligonucleotide properties calculator. 43-46
  
• Peng Jiang, Haonan Wu, Jiawei Wei, Fei Sang, Xiao Sun, Zuhong Lu:
  RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features. 47-51
  
• Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel:
  CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. 52-57
  
• Roy Eric Collins, Gabrielle Rocap:
  REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis. 58-62
  
• Ming-Fang Tsai, Yi-Jung Lin, Yu-Chang Cheng, Kuo-Hsi Lee, Cheng-Chih Huang, Yuan-Tsong Chen, Adam Yao:
  PrimerZ: streamlined primer design for promoters, exons and human SNPs. 63-65
  
• Yung-fu Chen, Rung Ching Chen, Lin Yu Tseng, Elong Lin, Yung-Kuan Chan, Ren-Hao Pan:
  NTMG (N-terminal Truncated Mutants Generator for cDNA): an automatic multiplex PCR assays design for generating various N-terminal truncated cDNA mutants. 66-70
  
• Andreas Untergasser, Harm Nijveen, Xiangyu Rao, Ton Bisseling, René Geurts, Jack A. M. Leunissen:
  Primer3Plus, an enhanced web interface to Primer3. 71-74
  
• Ramón Díaz-Uriarte, Andreu Alibés, Edward R. Morrissey, Andrés Cañada, Oscar M. Rueda, Mariana L. Neves:
  Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite. 75-80
  
• Lucía Conde, David Montaner, Jordi Burguet-Castell, Joaquín Tárraga, Ignacio Medina, Fátima Al-Shahrour, Joaquín Dopazo:
  ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. 81-85
  
• Hubert Rehrauer, Stefan Zoller, Ralph Schlapbach:
  MAGMA: analysis of two-channel microarrays made easy. 86-90
  
• Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquín Dopazo:
  FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. 91-96
  
• Hong-Yu Ou, Xinyi He, Ewan M. Harrison, Bridget R. Kulasekara, Ali Bin Thani, Aras Kadioglu, Stephen Lory, Jay C. D. Hinton, Michael R. Barer, Zixin Deng, Kumar Rajakumar:
  MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. 97-104
  
• Yue Lu, Xin He, Sheng Zhong:
  Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease. 105-114
  
• Deepak Grover, Alonzo S. Woodfield, Ranjana Verma, Peter P. Zandi, Douglas F. Levinson, James B. Potash:
  QuickSNP: an automated web server for selection of tagSNPs. 115-120
  
• Hongkun Zheng, Junjie Shi, Xiaodong Fang, Yuan Li, Søren Vang, Wei Fan, Junyi Wang, Zhang Zhang, Wen Wang, Karsten Kristiansen, Jun Wang:
  FGF: A web tool for Fishing Gene Family in a whole genome database. 121-125
  
• Pere Puigbò, Eduard Guzmán, Antoni Romeu, Santiago Garcia-Vallvé:
  OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. 126-131
  
• Michael C. Angellotti, Shafquat B. Bhuiyan, Guorong Chen, Xiu-Feng Wan:
  CodonO: codon usage bias analysis within and across genomes. 132-136
  
• Chun Liang, Gang Wang, Lin Liu, Guoli Ji, Yuansheng Liu, Jinqiao Chen, Jason S. Webb, Greg J. Reese, Jeffrey F. D. Dean:
  WebTraceMiner: a web service for processing and mining EST sequence trace files. 137-142
  
• Shivashankar H. Nagaraj, Nandan Deshpande, Robin B. Gasser, Shoba Ranganathan:
  ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform. 143-147
  
• Rowan A. C. Mitchell, Nathalie Castells-Brooke, Jan Taubert, Paul Verrier, David J. Leader, Christopher J. Rawlings:
  Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence. 148-151
  
• Yan Zhang, Shiuh-Ming Luoh, Lawrence S. Hon, Robert Baertsch, William I. Wood, Zemin Zhang:
  GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database. 152-158
  
• Byungwook Lee, Taehui Hong, Sang Jin Byun, Taeha Woo, Yoon Jeong Choi:
  ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences. 159-162
  
• Tomás Norambuena, Rodrigo Malig, Francisco Melo:
  SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation. 163-168
  
• Da Wei Huang, Brad T. Sherman, Qina Tan, Joseph Kir, David Liu, David Bryant, Yongjian Guo, Robert M. Stephens, Michael W. Baseler, H. Clifford Lane, Richard A. Lempicki:
  DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. 169-175
  
• Nicolas Goffard, Georg Weiller:
  PathExpress: a web-based tool to identify relevant pathways in gene expression data. 176-181
  
• Yuki Moriya, Masumi Itoh, Shujiro Okuda, Akiyasu C. Yoshizawa, Minoru Kanehisa:
  KAAS: an automatic genome annotation and pathway reconstruction server. 182-185
  
• Christina Backes, Andreas Keller, Jan Küntzer, Benny Kneissl, Nicole Comtesse, Yasser A. Elnakady, Rolf Müller, Eckart Meese, Hans-Peter Lenhof:
  GeneTrail - advanced gene set enrichment analysis. 186-192
  
• Jüri Reimand, Meelis Kull, Hedi Peterson, Jaanus Hansen, Jaak Vilo:
  g: Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments. 193-200
  
• Christoph D. Schmid, Thierry Sengstag, Philipp Bucher, Mauro Delorenzi:
  MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data. 201-205
  
• Purvesh Khatri, Calin Voichita, Khalid Kattan, Nadeem Ansari, Avani Khatri, Constantin Georgescu, Adi L. Tarca, Sorin Draghici:
  Onto-Tools: new additions and improvements in 2006. 206-211
  
• Carolina Perez-Iratxeta, Peer Bork, Miguel A. Andrade-Navarro:
  Update of the G2D tool for prioritization of gene candidates to inherited diseases. 212-216
  
• Katherine A. Romer, Guy-Richard Kayombya, Ernest Fraenkel:
  WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches. 217-220
  
• Huai-Kuang Tsai, Meng-Yuan Chou, Ching Hua Shih, Grace Tzu-Wei Huang, Tien-Hsien Chang, Wen-Hsiung Li:
  MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. 221-226
  
• Toshiyuki Okumura, Hiroki Makiguchi, Yuko Makita, Riu Yamashita, Kenta Nakai:
  Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. 227-231
  
• William A. Thompson, Lee Aaron Newberg, Sean Conlan, Lee Ann McCue, Charles E. Lawrence:
  The Gibbs Centroid Sampler. 232-237
  
• Li-Wei Chang, Burr R. Fontaine, Gary D. Stormo, Rakesh Nagarajan:
  PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. 238-244
  
• Shannan J. Ho Sui, Debra L. Fulton, David J. Arenillas, Andrew T. Kwon, Wyeth W. Wasserman:
  oPOSSUM: integrated tools for analysis of regulatory motif over-representation. 245-252
  
• Shaun Mahony, Panayiotis V. Benos:
  STAMP: a web tool for exploring DNA-binding motif similarities. 253-258
  
• Jonathan M. Carlson, Arijit Chakravarty, Charles E. DeZiel, Robert H. Gross:
  SCOPE: a web server for practical de novo motif discovery. 259-264
  
• Zhao Xu, Hao Wang:
  LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. 265-268
  
• Jean-François Lucier, Jonathan Perreault, Jean-François Noël, Gilles Boire, Jean-Pierre Perreault:
  RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures. 269-274
  
• Guoqing Lu, Thaine W. Rowley, Rebecca Garten, Ruben O. Donis:
  FluGenome: a web tool for genotyping influenza A virus. 275-279
  
• Yiming Bao, Pavel Bolotov, Dmitry Dernovoy, Boris Kiryutin, Tatiana A. Tatusova:
  FLAN: a web server for influenza virus genome annotation. 280-284
  
• Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount:
  SplicePort - An interactive splice-site analysis tool. 285-291
  
• Zoé Lacroix, Christophe Legendre, Louiqa Raschid, Ben Snyder:
  BIPASS: BioInformatics Pipeline Alternative Splicing Services. 292-296
  
• Sylvain Foissac, Michael Sammeth:
  ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. 297-299
  
• Mugdha Khaladkar, Vivian Bellofatto, Jason Tsong-Li Wang, Bin Tian, Bruce A. Shapiro:
  RADAR: a web server for RNA data analysis and research. 300-304
  
• Eva Freyhult, Vincent Moulton, Peter Clote:
  RNAbor: a web server for RNA structural neighbors. 305-309
  
• Anke Busch, Rolf Backofen:
  INFO-RNA - a server for fast inverse RNA folding satisfying sequence constraints. 310-313
  
• Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang:
  RSRE: RNA structural robustness evaluator. 314-319
  
• Jens Reeder, Peter Steffen, Robert Giegerich:
  pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. 320-324
  
• Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan, Süleyman Cenk Sahinalp:
  taveRNA: a web suite for RNA algorithms and applications. 325-329
  
• Alexander Kaiser, Jan Krüger, Dirk Evers:
  RNA Movies 2: sequential animation of RNA secondary structures. 330-334
  
• Andreas R. Gruber, Richard Neuböck, Ivo L. Hofacker, Stefan Washietl:
  The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. 335-338
  
• Peng Jiang, Haonan Wu, Wenkai Wang, Wei Ma, Xiao Sun, Zuhong Lu:
  MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. 339-344
  
• Lei Kong, Yong Zhang, Zhi-Qiang Ye, Xiao-Qiao Liu, Shuqi Zhao, Liping Wei, Ge Gao:
  CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. 345-349
  
• Helena Tåquist, Yuanyuan Cui, David H. Ardell:
  TFAM 1.0: an online tRNA function classifier. 350-353
  
• Jianlin Cheng:
  DOMAC: an accurate, hybrid protein domain prediction server. 354-356
  
• Harianto Tjong, Sanbo Qin, Huan-Xiang Zhou:
  PI²PE: protein interface/interior prediction engine. 357-362
  
• Narcis Fernandez-Fuentes, Carlos J. Madrid-Aliste, Brajesh Kumar Rai, J. Eduardo Fajardo, András Fiser:
  M4T: a comparative protein structure modeling server. 363-368
  
• Björn Wallner, Per Larsson, Arne Elofsson:
  Pcons.net: protein structure prediction meta server. 369-374
  
• Ian W. Davis, Andrew Leaver-Fay, Vincent B. Chen, Jeremy N. Block, Gary J. Kapral, Xueyi Wang, Laura Weston Murray, W. Bryan Arendall III, Jack Snoeyink, Jane S. Richardson, David C. Richardson:
  MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. 375-383
  
• Alper Uzun, Chesley M. Leslin, Alexej Abyzov, Valentin A. Ilyin:
  Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. 384-392
  
• Marc A. Martí-Renom, Ursula Pieper, Mallur S. Madhusudhan, Andrea Rossi, Narayanan Eswar, Fred P. Davis, Fátima Al-Shahrour, Joaquín Dopazo, Andrej Sali:
  DBAli tools: mining the protein structure space. 393-397
  
• Kengo Kinoshita, Yoichi Murakami, Haruki Nakamura:
  eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. 398-402
  
• Christian X. Weichenberger, Manfred J. Sippl:
  NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures. 403-406
  
• Markus Wiederstein, Manfred J. Sippl:
  ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. 407-410
  
• Stefan J. Suhrer, Markus Gruber, Manfred J. Sippl:
  QSCOP-BLAST - fast retrieval of quantified structural information for protein sequences of unknown structure. 411-415
  
• Allegra Via, Daniele Peluso, Pier Federico Gherardini, Emanuele de Rinaldis, Teresa Colombo, Gabriele Ausiello, Manuela Helmer-Citterich:
  3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. 416-419
  
• Yan-Long Lai, Shih-Chung Yen, Sung-Huan Yu, Jenn-Kang Hwang:
  pKNOT: the protein KNOT web server. 420-424
  
• Grigory Kolesov, Peter Virnau, Mehran Kardar, Leonid A. Mirny:
  Protein knot server: detection of knots in protein structures. 425-428
  
• Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer:
  Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. 429-432
  
• Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Jörg Hau, Olivier Martin, Dmitri Kuznetsov, Laurent Falquet:
  MyHits: improvements to an interactive resource for analyzing protein sequences. 433-437
  
• Chi-Hua Tung, Jinn-Moon Yang:
  fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. 438-443
  
• Coral del Val, Peter Ernst, Mechthild Falkenhahn, C. Fladerer, Karl-Heinz Glatting, Sándor Suhai, Agnes Hotz-Wagenblatt:
  ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ. 444-450
  
• Enrico Ferraro, Daniele Peluso, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich:
  SH3-Hunter: discovery of SH3 domain interaction sites in proteins. 451-454
  
• Norman E. Davey, Richard J. Edwards, Denis C. Shields:
  The SLiMDisc server: short, linear motif discovery in proteins. 455-459
  
• Takashi Ishida, Kengo Kinoshita:
  PrDOS: prediction of disordered protein regions from amino acid sequence. 460-464
  
• Chung-Tsai Su, Chien-Yu Chen, Chen-Ming Hsu:
  iPDA: integrated protein disorder analyzer. 465-472
  
• K. G. Tina, Rana Bhadra, Narayanaswamy Srinivasan:
  PIC: Protein Interactions Calculator. 473-476
  
• Joel Franklin, Patrice Koehl, Sebastian Doniach, Marc Delarue:
  MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape. 477-482
  
• Ludovic Autin, Pierre Tufféry:
  PMG: online generation of high-quality molecular pictures and storyboarded animations. 483-488
  
• C. Axel Innis:
  siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins. 489-494
  
• K. Anton Feenstra, Walter Pirovano, Klaas Krab, Jaap Heringa:
  Sequence harmony: detecting functional specificity from alignments. 495-498
  
• Harpreet Kaur Saini, Daniel Fischer:
  FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments. 499-502
  
• Kshama Goyal, Debasisa Mohanty, Shekhar C. Mande:
  PAR-3D: a server to predict protein active site residues. 503-505
  
• Adi Stern, Adi Doron-Faigenboim, Elana Erez, Eric Martz, Eran Bacharach, Tal Pupko:
  Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. 506-511
  
• Clifford E. Felder, Jaime Prilusky, Israel Silman, Joel L. Sussman:
  A server and database for dipole moments of proteins. 512-521
  
• Todd J. Dolinsky, Paul Czodrowski, Hui Li, Jens E. Nielsen, Jan H. Jensen, Gerhard Klebe, Nathan A. Baker:
  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. 522-525
  
• Shula Shazman, Gershon Celniker, Omer Haber, Fabian Glaser, Yael Mandel-Gutfreund:
  Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces. 526-530
  
• Mark V. Berjanskii, David S. Wishart:
  The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. 531-537
  
• Jin-Rui Xu, Jing-Xian Zhang, Bu-Cong Han, Liang Liang, Zhi Liang Ji:
  CytoSVM: an advanced server for identification of cytokine-receptor interactions. 538-542
  
• Hani Neuvirth, Uri Heinemann, David Birnbaum, Naftali Tishby, Gideon Schreiber:
  ProMateus - an open research approach to protein-binding sites analysis. 543-548
  
• Narendra Kumar, Debasisa Mohanty:
  MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes. 549-555
  
• P. Christoph Champ, Carlos J. Camacho:
  FastContact: a free energy scoring tool for protein-protein complex structures. 556-560
  
• Yung-Chiang Chen, Yu-Shu Lo, Wen-Chang Hsu, Jinn-Moon Yang:
  3D-partner: a web server to infer interacting partners and binding models. 561-567
  
• T. Bohme Leite, D. Gomes, Maria A. Miteva, Jacques Chomilier, Bruno O. Villoutreix, Pierre Tufféry:
  Frog: a FRee Online druG 3D conformation generator. 568-572
  
• Gonzalo López, Alfonso Valencia, Michael L. Tress:
  firestar - prediction of functionally important residues using structural templates and alignment reliability. 573-577
  
• Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, Robert L. Jernigan, Vasant Honavar, Drena Dobbs:
  RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. 578-584
  
• Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C. J. Adams-Collier, Kenta Nakai:
  WoLF PSORT: protein localization predictor. 585-587
  
• Yung-Hao Wong, Tzong-Yi Lee, Han-Kuen Liang, Chia-Mao Huang, Ting-Yuan Wang, Yi-Huan Yang, Chia-Huei Chu, Hsien-Da Huang, Ming-Tat Ko, Jenn-Kang Hwang:
  KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. 588-594
  
• Joshua S. Kaminker, Yan Zhang, Colin K. Watanabe, Zemin Zhang:
  CanPredict: a computational tool for predicting cancer-associated missense mutations. 595-598
  
• Jeffry D. Sander, Peter Zaback, J. Keith Joung, Daniel F. Voytas, Drena Dobbs:
  Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. 599-605
  
• Eoin Fahy, Manish Sud, Dawn Cotter, Shankar Subramaniam:
  LIPID MAPS online tools for lipid research. 606-612
  
• Thomas Handorf, Oliver Ebenhöh:
  MetaPath Online: a web server implementation of the network expansion algorithm. 613-618
  
• Jost Degenhardt, Martin Haubrock, Jürgen Dönitz, Edgar Wingender, Torsten Crass:
  DEEP - A tool for differential expression effector prediction. 619-624
  
• Zhenjun Hu, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M. Stuart, Charles DeLisi:
  VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. 625-632
  
• Feng-Chi Chen, Chuang-Jong Chen, Trees-Juen Chuang:
  INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events. 633-638
  
• Yun Sheng Chung, Wei-Hsun Lee, Chuan Yi Tang, Chin Lung Lu:
  RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints. 639-644
  
• Sébastien Moretti, Fabrice Armougom, Iain M. Wallace, Desmond G. Higgins, C. Victor Jongeneel, Cédric Notredame:
  The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. 645-648
  
• Jimin Pei, Bong-Hyun Kim, Ming Tang, Nick V. Grishin:
  PROMALS web server for accurate multiple protein sequence alignments. 649-652
  
• Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin:
  COMPASS server for remote homology inference. 653-658
  
• Fabrizio Ferrè, Yann Ponty, W. A. Lorenz, Peter Clote:
  DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. 659-668
  
• Michael Brudno, Alexander Poliakov, Simon Minovitsky, Igor Ratnere, Inna Dubchak:
  Multiple whole genome alignments and novel biomedical applications at the VISTA portal. 669-674
  
• Satish Chikkagoudar, Usman Roshan, Dennis R. Livesay:
  eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities. 675-677
  
• Yi Zhou, Laura F. Landweber:
  BLASTO: a tool for searching orthologous groups. 678-682
  
• Andreas Keller, Nicole Comtesse, Nicole Ludwig, Eckart Meese, Hans-Peter Lenhof:
  SePaCS - a web-based application for classification of seroreactivity profiles. 683-687
  
• Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, Rolf Backofen:
  BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data. 688-693
  
• Alvaro Martinez Barrio, Daniel Soeria-Atmadja, Anders Nistér, Mats G. Gustafsson, Ulf Hammerling, Erik Bongcam-Rudloff:
  EVALLER: a web server for in silico assessment of potential protein allergenicity. 694-700
  
• Leonid Zamdborg, Richard D. LeDuc, Kevin J. Glowacz, Yong-Bin Kim, Vinayak Viswanathan, Ian T. Spaulding, Bryan P. Early, Eric J. Bluhm, Shannee Babai, Neil L. Kelleher:
  ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry. 701-706
  
• Chuan-Yih Yu, Yin-Hao Tsui, Yi-Hwa Yian, Ting-Yi Sung, Wen-Lian Hsu:
  The Multi-Q web server for multiplexed protein quantitation. 707-712
  
• Sik Lok Lam:
  DSHIFT: a web server for predicting DNA chemical shifts. 713-717
  
• Trias Thireou, Vassilis Atlamazoglou, Manolis Levakis, Elias Eliopoulos, Athanassios Hountas, George Tsoucaris, Kostas Bethanis:
  CrystTwiV: a webserver for automated phase extension and refinement in X-ray crystallography. 718-722
  

Last update Mon Feb 13 04:54:43 2012 CET by the DBLP Team — Data released under the ODC-BY 1.0 license — See also our legal information page